1. The Basics Getting started with Perl for Bioinformatics programming

2. print "Welcome to the Wonderful World of Bioinformatics!\n"; Let's Get Started!

3. print "Welcome "; print "to "; print "the "; print "Wonderful "; print "World "; print "of "; print "Bioinformatics!"; print "\n"; Another version of welcome

4. Maxim 3.1 Programs execute in sequential order

5. Maxim 3.2 Less is better

6. Maxim 3.3 If you can say something with fewer words, then do so

7. $ perl -c welcome welcome syntax OK $ perl welcome Running Perl programs

8. String found where operator expected at welcome line 3, near "pint "Welcome to the Wonderful World of Bioinformatics!\n"" (Do you need to predeclare pint?) syntax error at welcome line 3, near "pint "Welcome to the Wonderful World of Bioinformatics!\n"" welcome had compilation errors. Running Perl – Syntax Errors

9. print ; "Welcome to the Wonderful World of Bioinformatics!\n"; Syntax and semantics $ perl whoops $ perl -c -w whoops Useless use of a constant in void context at whoops line 1. whoops syntax OK

10. $ chmod u+x welcome3 #! /usr/bin/perl -w $./welcome3 $ perl welcome3 Program: run thyself!

11. Maxim 3.4 There's more than one way to do it

12. Iteration

13. #! /usr/bin/perl -w # The 'forever' program - a (Perl) program, # which does not stop until someone presses Ctrl-C. use constant TRUE => 1; use constant FALSE => 0; while ( TRUE ) { print "Welcome to the Wonderful World of Bioinformatics!\n"; sleep 1; } Using the Perl while construct

14. $ chmod u+x forever $./forever Welcome to the Wonderful World of Bioinformatics!. Running forever...

15. Maxim 3.5 Add comments to make future maintenance of a program easier for other programmers and for you

16. Maxim 3.6 When using constant values, refer to them with a nice, human-friendly name as opposed to the actual value

17. Maxim 3.7 Use blocks to group program statements together

18. More Iterations

19. Maxim 3.8 A condition can result in a value of true or false

20. Introducing variable containers $name $_address $programming_101 $z $abc $count

21. Maxim 3.9 When you need to change the value of an item, use a variable container

22. Maxim 3.10 Don't be lazy: use good, descriptive names for variables

23. #! /usr/bin/perl -w # The 'tentimes' program - a (Perl) program, # which stops after ten iterations. use constant HOWMANY => 10; $count = 0; while ( $count < HOWMANY ) { print "Welcome to the Wonderful World of Bioinformatics!\n"; $count++; } Variable containers and loops

24. $ chmod u+x tentimes $./tentimes Welcome to the Wonderful World of Bioinformatics! Running tentimes...

25. Selection

26. #! /usr/bin/perl -w # The 'fivetimes' program - a (Perl) program, # which stops after five iterations. use constant TRUE => 1; use constant FALSE => 0; use constant HOWMANY => 5; $count = 0; while ( TRUE ) { $count++; print "Welcome to the Wonderful World of Bioinformatics!\n"; if ( $count == HOWMANY ) { last; } Using the Perl if construct

27. #! /usr/bin/perl -w # The 'oddeven' program - a (Perl) program, # which iterates four times, printing 'odd' when $count # is an odd number, and 'even' when $count is an even # number. use constant HOWMANY => 4; $count = 0; while ( $count < HOWMANY ) { $count++; if ( $count == 1 ) { print "odd\n"; } elsif ( $count == 2 ) { print "even\n"; } There Really Is MTOWTDI

28. elsif ( $count == 3 ) { print "odd\n"; } else # at this point $count is four. { print "even\n"; } The oddeven program, cont.

29. #! /usr/bin/perl -w # The 'terrible' program - a poorly formatted 'oddeven'. use constant HOWMANY => 4; $count = 0; while ( $count < HOWMANY ) { $count++; if ( $count == 1 ) { print "odd\n"; } elsif ( $count == 2 ) { print "even\n"; } elsif ( $count == 3 ) { print "odd\n"; } else # at this point $count is four. { print "even\n"; } } The terrible program

30. Maxim 3.11 Use plenty of whitespace, blank-lines and indentation to make your programs easier to read

31. #! /usr/bin/perl -w # The 'oddeven2' program - another version of 'oddeven'. use constant HOWMANY => 4; $count = 0; while ( $count < HOWMANY ) { $count++; if ( $count % 2 == 0 ) { print "even\n"; } else # $count % 2 is not zero. { print "odd\n"; } The oddeven2 program

32. print 5 % 2, "\n"; # prints a '1' on a line. print 4 % 2, "\n"; # prints a '0' on a line. print 7 % 4, "\n"; # prints a '3' on a line. Using the modulus operator

33. #! /usr/bin/perl -w # The 'oddeven3' program - yet another version of 'oddeven'. use constant HOWMANY => 4; $count = 0; while ( $count < HOWMANY ) { $count++; print "even\n" if ( $count % 2 == 0 ); print "odd\n" if ( $count % 2 != 0 ); } The oddeven3 program

34. <>; $line = <>; #! /usr/bin/perl -w # The 'getlines' program which processes lines. while ( $line = <> ) { print $line; } Processing Data Files

35. $ chmod u+x getlines $./getlines Running getlines...

36. $./getlines terrible $./getlines terrible welcome3 Asking getlines to do more

37. #! /usr/bin/perl -w # The 'patterns' program - introducing regular expressions. while ( $line = <> ) { print $line if $line =~ /even/; } Introducing Patterns

38. $./patterns terrible # The 'terrible' program - a poorly formatted 'oddeven'. { print "even\n"; } elsif ( $count == 3 ) { print "odd\n"; } { print "even\n"; } } $./patterns oddeven # The 'oddeven' program - a (Perl) program, # is an odd number, and 'even' when $count is an even print "even\n"; Running patterns...

39. Maxim 3.12 Patterns tell perl what to look for, not how to find it

40. Where To From Here